test replacing gpgr with ragg

umccr · Apr 3, 2024 · 64b6d0f · 64b6d0f
1 parent 8eb4484
commit 64b6d0f
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/.github/workflows/conda_docker_pkgdown.yml b/.github/workflows/conda_docker_pkgdown.yml
@@ -3,7 +3,7 @@ name: conda-docker-docs
 on:
   push:
     branches:
-      - deploy_0.5.0
+      - deps
       - rnasum-rpackage
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}

diff --git a/deploy/conda/recipe/meta.yaml b/deploy/conda/recipe/meta.yaml
@@ -30,7 +30,7 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-ragg
     - r-here
     - r-htmltools
     - r-htmlwidgets
@@ -70,7 +70,7 @@ requirements:
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-ragg
     - r-here
     - r-htmltools
     - r-htmlwidgets

diff --git a/inst/rmd/rnasum.Rmd b/inst/rmd/rnasum.Rmd
@@ -63,9 +63,9 @@ knitr::knit_hooks$set(timeit = local({
 knitr::opts_chunk$set(timeit = TRUE, echo = FALSE)
 ```
 
-```{r echo=TRUE, message=FALSE}
-#source(here::here("inst/rmd/params/pd.R")) # for use with 'Run All Chunks Above'
-#source(here::here("inst/rmd/params/sk.R")) # for use with 'Run All Chunks Above'
+```{r echo=FALSE, message=FALSE}
+# source(here::here("inst/rmd/params/pd.R")) # for use with 'Run All Chunks Above'
+# source(here::here("inst/rmd/params/sk.R")) # for use with 'Run All Chunks Above'
 
 # start with more exotic pkgs, then get to core ones
 {
@@ -1063,8 +1063,10 @@ for (dataset in names(ref_dataset.list)) {
   ##### Get genes genomic coordiantes
   ##### Limit genes annotation to those genes for which sample expression measurements are available
   gene_info <- tx_gene_id_105 |>
-    dplyr::select("GENEID", "GENEBIOTYPE", "GENENAME", "SEQNAME",
-        "GENESEQSTART", "GENESEQEND") |>
+    dplyr::select(
+      "GENEID", "GENEBIOTYPE", "GENENAME", "SEQNAME",
+      "GENESEQSTART", "GENESEQEND"
+    ) |>
     dplyr::rename("ENSEMBL" = "GENEID", "SYMBOL" = "GENENAME") |>
     dplyr::filter(.data$ENSEMBL %in% data.df$ENSEMBL)